Sequence
atgc intronic sequence ATGC exonic sequencegtttaataatatcctctctttggtttggcttacacactcactttcatgatatattgaagccatcttgtttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G06634.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G885700_T02 (Zea mays), 3'ss of exon 3
--------------gtttaataatatcctc------tctttggtttg---gcttacacactcactttcatgatatattgaagccatcttgtttttgttttt-tgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
| | | |||| |||| || || | | || | | | || || | || | | | | | | |||||||| | |||||||| |||||||||||||||| |||||||||||| ||||| | |||| | | || | ||||||| ||||| |||
gtactgtttataattcctggtcacatcccagagtaatcttcagtctgcaaaggcatgtttctatttcagttgcttgattaatcctttttctgctaaatctgattttgcagAAATTCTTAGATAGTTCTAAGTTGAAGAGACATTTTCTTATTCATACAGGAGAAAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAAG
upper sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G140016_T01 (Zea mays), 3'ss of exon 3
------------------------gtttaataata-tcctctctttggtttggcttacacactcactttcatgatat-attgaagccatcttgtttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
| | | || || || | || ||| | | || || | | | | | | | | | ||| | | |||||||| | ||||| || |||||||||||||||| |||||| ||||||||||||| |||| | | || | ||||||| ||||| | |
gtactgtttacccttccttttcacatcccagagtaatcttcagtctgcaaaggc--atggtcccatttcagttgcttgactaatcttttttcgggtaaatttgattttgcagAAATTCTTAGATAGCTCTAAGTTGAAGAGACATTTTCTTATCCATACTGGAGAGAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAGG
upper sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
----gtttaataatat-cctctctttggtttggcttaca--cactcactttcatgatatattga---agccatcttg----tttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
|||||| || || || | |||| | | ||| | ||| | | | ||| | || | ||| ||| | ||||||||||||||||| ||||||||||| ||||||| ||| |||||||| || ||||| ||| | | ||| || ||||||| ||||| |||
atttatttaatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
upper sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
-------gtttaataatatcctctc-tttggtttggcttacacactcactttcatgatatattga---agccatcttg----tttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
| || || | | | ||| | ||| | | ||| | ||| | | | ||| | || | ||| || | ||||||||||||||||| ||||||||||| ||||||| ||| |||||||| || ||||| ||| | | ||| || ||||||| ||||| |||
taatgctatgtatcaagttgcaatagcttgctgtggactgtg-gtttactctaatggcaggtctatttagcagtgctgaaagtattttgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
upper sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
--------gtttaataatatcctctctttggtttggcttacacactcactttcatgatatattgaagccatctt------gtttttgttttt-tgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
|||| || | ||| | |||| | | || || || | ||| | || | || |||| ||| || ||||||||| |||||||||||||| |||| ||||| | || |||||||| ||||||||| ||| | | ||| || ||||||| ||||| |||
cccataatgtttc-tattttccccacttttctctcatctaatttttctctgctccatcaggctgatgacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164142816|gb|ES036870.1|ES036870EST: GAGAAAGACAATATGTTTGTGATCAGGAAGGATGTGGAAAG AAATTTCTGGATAGTTCAAAGTTGAAGAGACA
genomic: GAGAAAGACAATATGTTTGTGATCAGGAAGGATGTGGAAAGgtttaataat ... tttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacactcactttcatgatatattgaagccatcttgtttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
cactcac putative branch site (score: 2)
tcttgtttttgttttt putative PPT
tttttgttttttgtaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaataatatcctctctttggtttggcttacacactcactttcatgatatattgaagccatcttgtttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG